AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_fusions005_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251077 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0030 62 oligopeptide ABC transporter, permease protein #1 TM0031 24 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #2 TM0032 300 transcriptional regulator, XylR-related #3 TM0122 247 ferric uptake regulation protein #4 TM0486 66 conserved hypothetical protein #5 TM0766 117 transcriptional regulator, GntR family #6 TM1132 155 moxR protein, putative #7 TM1135 83 branched chain amino acid ABC transporter, periplasmic amino acid-binding protein #8 TM1136 78 branched chain amino acid ABC transporter, permease protein #9 TM1222 55 oligopeptide ABC transporter, permease protein #10 TM1223 131 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #11 TM1301 185 astB/chuR-related protein #12 TM1632 62 conserved hypothetical protein Motif 1 CGGGTTCCACAAAAACAGAGTGGGGAGTGAGAATTGA 0 35 1 CTGAGGAAGATAGATAAGAAGCAGGAGGAATATGGA 2 274 1 TATAACATAGTATAATAGAACCGGGAGGG 4 0 0 TCAAATTAGAAGAGCCGAATTGAGGAGGTGGAAAA 4 41 1 AGATGATGAAATCAATTAAATCAGGAGGG 5 0 0 GTAATAGTATAATATTACAGCGAGGTGATAGATC 5 93 1 TTTTCAGAAGAAAAGATATTCCAGGAGGT 6 0 0 GAAGTATGCAAATACTTCTATCTGGAGGGATCCTCGG 6 128 1 AAAGGATTTCTTGACCGTTTCGTGGTGAGCCTGTAAAAT 7 16 1 AATACTTATAAAAATCATTCTCATGAGGGGAGGGAAGAG 7 52 1 TCAATCAAAGAAAGCGAAGCCCCTGAGGGGCCTCGCTTT 8 31 0 CTTCTTTTTTTAAAACCCCGCCCCGAGGGGCGGGGTCAT 9 14 0 ATTTTCACTGTACATTTACACGTGGAGATAGCGATCTCA 10 79 1 TATTAAGTACTCTACAAAAATGGGGTGGTTGT 11 163 1 TCGTTGTGTCTCCTTCCGGAGGGATTCAATATG 12 4 1 CAATATGTATTGTACAACACTGTGGAGGAACAGAAA 12 36 1 * * ** ****** MAP Score: 15.2859 Motif 2 TTTTTGTGGAACCCGGCCCCGAAGTGGGGC 0 20 0 AATGATGACCCCGCCCCTCGGGGCGGG 9 7 1 TTTTTTTAAAACCCCGCCCCGAGGGGCGGG 9 19 0 TCTTTTCCCGGCCCCACTTCGGGGC 0 5 1 ATCTCTTCCCTCCCCTCATGAGAAT 7 68 0 ********** MAP Score: 12.7695 Motif 3 AAGAGCCGAATTGAGGAGGTGGAAAA 4 50 1 AAGATAGATAAGAAGCAGGAGGAATATGGA 2 280 1 ATATTCCTAATAGAGAAGGCGGCCGCCTTCTT 11 116 0 GGGTTTTAAAAAAAGAAGGAGGTAGGAGTC 9 35 1 TAGAAATTTTTAAAGAAGGCGGCCGCCTTCTC 11 104 1 AAACCCCGCCCCGAGGGGCGGGGTCATCATT 9 9 0 GTACTCTACAAAAATGGGGTGGTTGT 11 169 1 AATCATTCTCATGAGGGGAGGGAAGAGAT 7 64 1 CCCGGCCCCGAAGTGGGGCCGGGAAAAGA 0 7 0 ATAGTATAATAGAACCGGGAGGG 4 1 0 TCATACTCTTTTAAGGGGGTGTTCTT 10 115 1 TGAAATCAATTAAATCAGGAGGG 5 1 0 GCTCCTTGGAAAGAGCATCGGGAATAAAATCA 2 113 1 TCTCAAAGTGAGAAGAATGTGTGTAACAAAAA 2 72 0 * ******* ** MAP Score: 9.56972 Motif 4 TCAAAGAAAATATTAGAATTTGAACTATAATTCGAAATA 2 153 1 TGAGTCATATCGTTATAATTTCTTTCTGAGGAAGATAGA 2 249 1 TACCGTATTATGGTATAATGAAAATGGATGGCAGATGTC 3 92 0 TACCATAATACGGTATAATCGGAGAGCACGATGAATACT 3 116 1 AATATATCATCAGTACAATGTTTGAATGATATCTTGAAA 3 159 1 CGACTGTGTGTAGTACAATATAACTTGCAAATGCTTTGC 3 202 1 AATTATAACATAGTATAATAGAACCGGGAGGG 4 3 0 TATTATACTATGTTATAATTCAAATTAGAAGAGCCGAAT 4 22 1 TGTTGCGTTTTGTTAAAATAGATGATGAAATCAATTAAA 5 19 0 AGTAGTGTAATAGTATAATATTACAGCGAGGTGATAGAT 5 87 1 GAAATTTCTGCATTAAAATTCAACGTGTATTCGAAAAAT 6 58 1 CGTGGTGAGCCTGTAAAATACTTATAAAAATCATTCTCA 7 36 1 CTCCACAGTGTTGTACAATACATATTGAATCCCTCCGGA 12 24 0 ***** *** * * MAP Score: 7.67594 Motif 5 GAACCCGGCCCCGAAGTGGGGCCGGGAAAAGA 0 8 0 TCCACAAAAACAGAGTGGGGAGTGAGAATTGA 0 40 1 ATTAGAAGAGCCGAATTGAGGAGGTGGAAAA 4 45 1 TATAATATTACAGCGAGGTGATAGATC 5 100 1 TGATTGAAGAAAGGAAGGTGAAAGA 8 63 1 AAACCCCGCCCCGAGGGGCGGGGTCATCATT 9 7 0 GGTTTTAAAAAAAGAAGGAGGTAGGAGTC 9 36 1 CTGTACATTTACACGTGGAGATAGCGATCTCATA 10 86 1 AGAAATTTTTAAAGAAGGCGGCCGCCTTCTCTAT 11 105 1 AAGTACTCTACAAAAATGGGGTGGTTGT 11 167 1 TTGAATCCCTCCGGAAGGAGACACAACGA 12 5 0 ATGTATTGTACAACACTGTGGAGGAACAGAAA 12 40 1 ***** ** ** * MAP Score: 7.10106 Motif 6 TTTCCCGGCCCCACTTCGGGGCCGGGTTCCACAA 0 13 1 AAAAATCATTCTCATGAGGGGAGGGAAGAGAT 7 61 1 GATGACCCCGCCCCTCGGGGCGGGGTTTTAAAAA 9 13 1 ATCTCATACTCTTTTAAGGGGGTGTTCTT 10 112 1 TATGCAAATACTTCTATCTGGAGGGATCCTCGG 6 132 1 ATGTATTGTACAACACTGTGGAGGAACAGAAA 12 40 1 CCATTCTATTCCTTTAGGTGGATGCACTAACAGA 11 32 1 AAGTACTCTACAAAAATGGGGTGGTTGT 11 167 1 AAAAGCGAGGCCCCTCAGGGGCTTCGCTTTCTTT 8 30 1 ATTAGAAGAGCCGAATTGAGGAGGTGGAAAA 4 45 1 GATTTCTTGACCGTTTCGTGGTGAGCCTGTAAAA 7 20 1 TCGTTGTGTCTCCTTCCGGAGGGATTCAATATG 12 9 1 CCTAGATATTCCTAATAGAGAAGGCGGCCGCCTT 11 119 0 ** ** **** ** MAP Score: 5.66941 Motif 7 CATCGGGAATAAAATCAGTTGTAACTCAAAGAAA 2 128 1 AATTTGAACTATAATTCGAAATAATTCCTGTTAT 2 169 1 AAGATAGATAAGAAGCAGGAGGAATATGGA 2 280 1 TCATTATACCATAATACGGTATAATCGGAGAGCA 3 110 1 AGCACGATGAATACTGAGAAATATATCATCAGTA 3 140 1 CGGTTCTATTATACTATGTTATAATTCAAATTAG 4 16 1 CGAAAAATTGAGAATTTGATAGAAAAACTGGTAT 6 89 1 AAAAACTGGTATACTTTGAAGTATGCAAATACTT 6 111 1 GTTGTTGCAAATAATCAGAAATAAATCTTGATAA 10 16 1 GTATTGTACAACACTGTGGAGGAACAGAAA 12 42 1 * *** * ***** MAP Score: 5.10108 Motif 8 AAATCCATCGAAATCATAAGTTATTGACTC 2 44 0 AGCATCGGGAATAAAATCAGTTGTAACTCA 2 126 1 TCATAATCATAAAAAATGAGTATTACTCGT 2 207 1 TGAGGAAGATAGATAAGAAGCAGGAGGAAT 2 275 1 GTTAAAACAAAAATCAGGAG 3 0 0 ACTGAGAAATATATCATCAGTACAATGTTT 3 152 1 GTTATAATTCAAATTAGAAGAGCCGAATTG 4 33 1 GAAATCAATTAAATCAGGAGGG 5 2 0 CGGGGTTTTAAAAAAAGAAGGAGGTAGGAG 9 33 1 AAGTTGTTGCAAATAATCAGAAATAAATCT 10 14 1 ********** MAP Score: 5.02958 Motif 9 AATATTAGAATTTGAACTATAATTCGAAATA 2 161 1 CTGATTTTTGTTTTAACAAAGTTATATTTTC 3 13 1 CAGTACAATGTTTGAATGATATCTTGAAATC 3 169 1 GCTCTTCTAATTTGAATTATAACATAGTATA 4 25 0 TCATCATCTATTTTAACAAAACGCAACAAAA 5 30 1 ACACGTTGAATTTTAATGCAGAAATTTCGCC 6 55 0 AAATTGAGAATTTGATAGAAAAACTGGTATA 6 93 1 ACTGGTATACTTTGAAGTATGCAAATACTTC 6 115 1 CTTCGCTTTCTTTGATTGAAGAAAGGAAGGT 8 51 1 CGGGGCGGGGTTTTAAAAAAAGAAGGAGGTA 9 28 1 GGTTAGAAATTTTTAAAGAAGGCGGCCGCCT 11 101 1 ****** **** MAP Score: 4.67217 Motif 10 CTCCCCACTCTGTTTTTGTGGAACCCGGCCCCGAA 0 27 0 ATTTCGATGGATTTTTTGTTACACACATTCTTCTC 2 60 1 CTCCTGATTTTTGTTTTAACAAAGTTATATTTT 3 8 1 TTTAACAAAGTTATATTTTCTAAAATAAACCCCTT 3 24 1 CATTTGCAAGTTATATTGTACTACACACAGTCGCT 3 200 0 TGATTTCATCATCTATTTTAACAAAACGCAACAAA 5 25 1 CTGGAATATCTTTTCTTCTGAAAAATTATACACCA 6 15 1 AAAGTATACCAGTTTTTCTATCAAATTCTCAATTT 6 93 0 TCCTACCTCCTTCTTTTTTTAAAACCCCGCCCCGA 9 27 0 GGGATTCAATATGTATTGTACAACACTGTGGAGGA 12 30 1 TTTCTGTTCCTCCACAGTGTTGTACA 12 46 0 ** * ** * **** MAP Score: 2.69897 Motif 11 TCAAAGTGAGAAGAATGTGTGTAACAAAAAATCC 2 68 0 TTCTCACTTTGAGAATGTCTTGAGCTCCTTGGAA 2 90 1 CATAATCATAAAAAATGAGTATTACTCGTGTTTG 2 208 1 ATGGTATAATGAAAATGGATGGCAGATGTCGTAT 3 88 0 CTTGAAATCAGCGACTGTGTGTAGTACAATATAA 3 191 1 AATATAACTTGCAAATGCTTTGCATTTGCAGGTG 3 218 1 CTCCCCTCATGAGAATGATTTTTATAAGTATTTT 7 50 0 ATAATCCCGGGAGACTGGATTTGGAATGTAAACA 10 46 1 CCTAAAGGAATAGAATGGTTCGCGATTCGCTTAA 11 16 0 ******* * * * MAP Score: 2.13122 Motif 12 CACAAAAACAGAGTGGGGAGTGAGAATTGA 0 42 1 TTTGCATTTGCAGGTGAGAGT 3 236 1 CCGAATTGAGGAGGTGGAAAA 4 55 1 ATATTACAGCGAGGTGATAGATC 5 104 1 TCATTCTCATGAGGGGAGGGAAGAGAT 7 66 1 TGAAGAAAGGAAGGTGAAAGA 8 67 1 AAAAAAGAAGGAGGTAGGAGTC 9 43 1 TCCTTAGACTGAGGTTAGAAATTTTTAAAG 11 89 1 ********** MAP Score: 1.87971 Motif 13 AACAGAGTGGGGAGTGAGAATTGA 0 48 1 ATCATTACATGGAGTCAATAACTTATGATT 2 33 1 ATATTTTCTTTGAGTTACAACTGATTTTAT 2 136 0 TTTATGATTATGAGTGAATAACAGGAATTA 2 190 0 TCTCATGAGGGGAGGGAAGAGAT 7 70 1 TCGCTTTCTTTGATTGAAGAAAGGAAGGTG 8 53 1 AAAAAAAGAAGGAGGTAGGAGTC 9 42 1 TCCTTTAGGTGGATGCACTAACAGAAGTCA 11 41 1 CTCAGTCTAAGGAGTTACTACTGCACATCT 11 72 0 CCTTCCGGAGGGATTCAATATGTATTGTAC 12 21 1 ********** MAP Score: 1.82086 Motif 14 CGGGGCCGGGTTCCACAAAAACAGAGTGGGGAGT 0 29 1 AGAATGTGTGTAACAAAAAATCCATCGAAATCAT 2 57 0 TCACTCATAATCATAAAAAATGAGTATTACTCGT 2 203 1 CTTATCTATCTTCCTCAGAAAGAAATTATAACGA 2 258 0 CTGAGGAAGATAGATAAGAAGCAGGAGGAATATG 2 274 1 AATAAACCCCTTAAAAAAATCGAAGAACTCAGCT 3 47 1 CATCATCTATTTTAACAAAACGCAACAAAACACG 5 31 1 TCAACGTGTATTCGAAAAATTGAGAATTTGATAG 6 77 1 TCCTTTCTTCAATCAAAGAAAGCGAAGCCCCTGA 8 44 0 CGGGGCGGGGTTTTAAAAAAAGAAGGAGGTAGGA 9 28 1 AGAAAAGTTGTTGCAAATAATCAGAAATAAATCT 10 10 1 GGTTAGAAATTTTTAAAGAAGGCGGCCGCCTTCT 11 101 1 TAGATATTCCTAATAGAGAAGGCGGCCGCCTTCT 11 117 0 * ****** *** MAP Score: 0.102092